Outcome of Communication Training in Veterinary Studies: Influence on the Perception of the Relevance of Veterinary Competencies and Self-Assessment of Communication Skills

Since communication skills contribute significantly to professional success among veterinarians, there is a particular focus on developing communication classes in veterinary curricula. At Freie Universität Berlin, an e-learning course covering the basics of communication and a practical communication course based on role plays with and without simulation persons have been established. The outcome of these communication courses on the assessment of the relevance of several veterinary competencies and on the self-assessment of communication skills using the SE-12 questionnaire was investigated. For this purpose, students were surveyed before and after the e-learning course as well as before and after the practical course. Veterinarians were also surveyed on the relevance of veterinary competencies. The relevance of communicative competencies for professional success was rated significantly higher by the students after completing the practical course than by the other students and the veterinarians. Self-assessment of communication skills showed little increase after the e-learning course, but a significant increase after the practical course. Thus, an effective outcome of the communication classes was observed mainly after the practical course. However, the effect of the e-learning course cannot be ruled out since the students participating in the practical course have also completed the e-learning course beforehand.

"Do not look at me like that": Is the facial expression score reliable and accurate to evaluate pain in large domestic animals? A systematic review

Introduction

Facial expression scoring has proven to be useful for pain evaluation in humans. In the last decade, equivalent scales have been developed for various animal species, including large domestic animals. The research question of this systematic review was as follows: is facial expression scoring (intervention) a valid method to evaluate pain (the outcome) in large domestic animals (population)?

Method

We searched two databases for relevant articles using the search string: "grimace scale" OR "facial expression" AND animal OR "farm animal" NOT "mouse" NOT "rat" NOT "laboratory animal." The risk of bias was estimated by adapting the Quality Assessment of Diagnostic Accuracy Studies (QUADAS) checklist.

Results

The search strategy extracted 30 articles, with the major share on equids and a considerable number on cows, pigs, and sheep. Most studies evaluated facial action units (FAUs), including the eye region, the orbital region, the cheek or the chewing muscles, the lips, the mouth, and the position of the ears. Interobserver reliability was tested in 21 studies. Overall FAU reliability was substantial, but there were differences for individual FAUs. The position of the ear had almost perfect interobserver reliability (interclass coefficient (ICC): 0.73-0.97). Validity was tested in five studies with the reported accuracy values ranging from 68.2 to 80.0%.

Discussion

This systematic review revealed that facial expression scores provide an easy method for learning and reliable test results to identify whether an animal is in pain or distress. Many studies lack a reference standard and a true control group. Further research is warranted to evaluate the test accuracy of facial expression scoring as a live pen side test.

Integration and potential of teaching communication skills in the study of veterinary medicine in Germany

Goal: Presentation of the current range of courses regarding communication at the five German educational institutions for veterinary medicine. In addition to learning objectives and individual solutions, possible potential for future developments are presented. Methods: Interviews with communication educators at the five German education institutions and subsequent synopsis. Results: To date, there are no binding education guidelines regarding communication in veterinary medicine. Nevertheless, communication education has been introduced at all five education institutions, albeit depth and formats vary considerably. The learning objectives are largely consistent and based on the recommendations for day-one-skills made by the European Association of Establishments for Veterinary Education. Communication is not recognized as a fully-fledged subject in the curricula of any of the education institutions. All education institutions clearly fall short of teaching the recommended 150 lecture hours. Conclusion: To ensure communication skills in veterinary medicine graduates, binding education guidelines should be agreed upon. Communication education should be integrated into all veterinary curricula as a fully-fledged subject with longitudinally increasing depth.

An Exploratory Study on the Central Nervous Correlates of Sexual Excitation and Sexual Inhibition

The Sexual Inhibition/Sexual Excitation Scales (SIS/SES) measure sexual excitation and sexual inhibition proneness. We used SIS and SES scores of 62 heterosexual teleiophilic men (M_age 34.3, SD = 9.9) to predict brain activation levels during the presentation of male and female visual sexual stimuli in a magnetic resonance imaging (MRI) scanner. Statistical analyses revealed significant correlations. SES and SIS1 scores were positively associated with brain activation in various brain regions during the presentation of both male and female stimuli. SIS2 turned out to be a weaker predictor of brain activation, still revealing one significant correlation in the right lateral orbitofrontal cortex. Significant regions for SES and SIS1 were, among others, primary and supplementary motor areas, the caudate nucleus, the dorsal anterior cingulate cortex, anterior insula, and prefrontal areas. Our study can be seen as an exploratory investigation of SIS and SES with means of functional brain imaging. The results provide a promising contribution to the assertion of neurophysiological systems of sexual inhibition and excitation proneness.

Minimum inhibitory concentrations of frequently used antibiotics against Escherichia coli and Trueperella pyogenes isolated from uteri of postpartum dairy cows

The objective of this study was to determine minimum inhibitory concentrations (MIC) of frequently used antimicrobials for Escherichia coli and Trueperella pyogenes isolated from postpartum bovine uteri of cows with acute puerperal metritis (APM, n = 67), cows suspected to have APM (n = 37), and healthy cows (n = 37) and to evaluate possible differences in MIC according to clinical signs. Cows with APM had reddish-brown, fetid vaginal discharge and rectal temperature (RT) ≥39.5°C within 21 d in milk; cows suspected to have APM had either reddish-brown, fetid vaginal discharge or RT ≥39.5°C within 21 d in milk; and healthy cows had neither fetid discharge nor RT ≥39.5°C. Samples were collected from cows on commercial dairy herds (n = 7) using the cytobrush technique. A total of 37 T. pyogenes isolates and 85 E. coli isolates were tested. Ceftiofur, a third-generation cephalosporin that is often used to treat APM, was the focus of analysis. Trueperella pyogenes and E. coli were isolated more often from samples of cows with APM (46 and 90%, respectively) compared with samples from healthy cows (19 and 54%, respectively). Regarding cows suspected to have APM, T. pyogenes and E. coli were numerically more often isolated (30 and 70%, respectively) than in healthy cows (19 and 54%, respectively). Minimum inhibitory concentrations of ceftiofur were low. For T. pyogenes and E. coli, MIC₅₀ (concentration that inhibited growth of 50% of isolates) were 0.25 and 0.5 µg/mL and MIC₉₀ (concentration that inhibited growth of 90% of isolates) were 0.5 and 1 µg/mL, respectively. Although ceftiofur inhibited all T. pyogenes at the highest concentration tested (64 µg/mL), the growth of 5.9% of E. coli was not impaired. Recently, ampicillin has been suggested as an alternative treatment for APM. Although the T. pyogenes isolates exhibited low MIC in general (MIC₅₀ ≤0.015 µg/mL and MIC₉₀ = 0.06 µg/mL) and 81.1% of all T. pyogenes could be inhibited at the lowest ampicillin concentration tested, 11.8% of the E. coli isolates were not impaired at the highest concentration (64 µg/mL) tested in this study. The MIC₅₀ and MIC₉₀ of E. coli were 4 and ≥128 µg/mL, respectively. We detected no difference in the MIC distributions of ceftiofur or ampicillin among isolates from the 3 APM groups. In summary, E. coli with high MIC against ceftiofur as well as against ampicillin were found in this study.

Efficacy of Non-steroidal Anti-inflammatory Drugs for the Treatment of Acute Puerperal Metritis in Dairy Cows

<p><strong>Background: </strong>Acute puerperal metritis (APM) is a potentially life threatening, painful disease and is often treated with third-generation cephalosporins (Machado et al., 2014; Stojkov et al., 2015). An increasing antibiotic resistance is well documented and associated with decreasing clinical efficacy, animal welfare and economic consequences (Thomson et al., 2004). Hence, there is the need to evaluate alternative therapies to antibiotics.</p><p><strong>Objective:</strong> The objective of this study was to assess the efficacy of ketoprofen for the treatment of APM compared with ceftiofur hydrochloride.</p><p><strong>Materials and Methods:</strong> A total of 610 dairy cows from 6 farms in Germany were enrolled. Inclusion criteria was a rectal temperature (RT) ≥ 39.5 °C and a reddish-brown fetid vaginal discharge within the first 10 DIM. Cows meeting the inclusion criteria were randomly allocated to treatment with ketoprofen (3 mg/kg of body weight, n = 300) or treatment with ceftiofur (1 mg/kg of body weight, n = 310), both administered on 3 consecutive days. Rectal temperature was recorded daily for a period of 7 days after enrollment. Cows that showed RT ≥ 39.5 °C on day 4 to 7 after inclusion received an extended treatment (extT) with ceftiofur for 3 (ketoprofen group) or 2 (ceftiofur group) more days. Between 21 and 40 DIM cows were examined with the metricheck device and vaginal discharge was categorized on a 5-point scale according to the presence of pus.</p><p><strong>Results:</strong> A total of 52 cows (35 from ketoprofen group, 17 from ceftiofur group) were excluded from analysis due to missing protocol compliance (n = 37) or concurrent disease (n = 15). Cows initially treated with ketoprofen had higher odds of extT than cows treated with ceftiofur (61% vs 31%, OR 3.47, P &lt; 0.01, n = 558). Occurrence of purulent vaginal discharge (PVD) was similar for both treatment groups. However, cows with extT had 2.12 (P &lt; 0.01, n = 438) times the odds of PVD than cows without extended treatment. Treatment group did not affect milk yield, first artificial insemination pregnancy risk, time to first AI and time to pregnancy.</p><p><strong>Conclusions:</strong> The results indicate that although cows initially treated with ketoprofen were more likely to receive extT, fewer doses of ceftiofur (1.83) were required compared with cows initially treated with ceftiofur (3.63). Consequently, there is considerable potential of reducing antimicrobial treatment by implementing a treatment protocol starting with ketoprofen.</p><br /> <img src="https://www.veterinaryevidence.org/rcvskmod/icons/oa-icon.jpg" alt="Open Access" />

Gray matter anomalies in pedophiles with and without a history of child sexual offending

Pedophilia is a psychiatric disorder that is inter-related with but distinct from child sexual offending (CSO). Neural alterations reportedly contribute to both pedophilia and CSO, but until now, no study has distinguished the brain structural anomalies associated with pedophilia from those specifically associated with CSO in pedophilic men. Using high-resolution T1-weighted brain images and voxel-based morphometry, we analyzed the gray matter (GM) volume of the following 219 men recruited at four acquisition sites in Germany: 58 pedophiles with a history of CSO, 60 pedophiles without any history of CSO and 101 non-pedophilic, non-offending controls to control for the effects of age, education level, verbal IQ, sexual orientation and the acquisition site. Although there were no differences in the relative GM volume of the brain specifically associated with pedophilia, statistical parametric maps revealed a highly significant and CSO-related pattern of above vs below the 'normal' GM volume in the right temporal pole, with non-offending pedophiles exhibiting larger volumes than offending pedophiles. Moreover, regression analysis revealed that the lower GM volume of the dorsomedial prefrontal or anterior cingulate cortex was associated with a higher risk of re-offending in pedophilic child molesters. We believe our data provide the first evidence that CSO in pedophilia rather than pedophilia alone is associated with GM anomalies and thus shed new light on the results of previous studies on this topic. These results indicate the need for new neurobehavioral theories on pedophilia and CSO and may be potentially useful for treatment or prevention approaches that aim to reduce the risk of (re)offending in pedophilia.

High potential for weathering and climate effects of non-vascular vegetation in the Late Ordovician

It has been hypothesized that predecessors of today's bryophytes significantly increased global chemical weathering in the Late Ordovician, thus reducing atmospheric CO₂ concentration and contributing to climate cooling and an interval of glaciations. Studies that try to quantify the enhancement of weathering by non-vascular vegetation, however, are usually limited to small areas and low numbers of species, which hampers extrapolating to the global scale and to past climatic conditions. Here we present a spatially explicit modelling approach to simulate global weathering by non-vascular vegetation in the Late Ordovician. We estimate a potential global weathering flux of 2.8 (km³ rock) yr⁻¹, defined here as volume of primary minerals affected by chemical transformation. This is around three times larger than today's global chemical weathering flux. Moreover, we find that simulated weathering is highly sensitive to atmospheric CO₂ concentration. This implies a strong negative feedback between weathering by non-vascular vegetation and Ordovician climate.

Early non-vascular vegetation may have caused an interval of glaciations in the Late Ordovician by enhancing global chemical weathering. Here, by simulating the organisms with a spatially explicit, process-based model, the authors propose that Ordovician vegetation had a high potential for chemical weathering.

A computational model of a human single sinoatrial node cell

For the investigation of the spontaneous rhythmical activity response in the application of cardiac neuromodulation, we formulated a human sinoatrial node (SAN) cell model. With the aim of decreasing elevated heart rate (HR), we want to establish a hardware-in-the-loop system including this model for the analysis of optimal stimulation patterns of the neurostimulation system. Base model structures are adopted from rabbit SAN cell models available in literature and conveyed with Hodgkin-Huxley-type model equations describing the complex time and voltage dependent activation and deactivation processes of individual ion channels. The resulting model consists of 15 currents which are currently known to be responsible for the generation of the membrane action potential (AP). The model reproduces AP frequencies equivalent to those measured in isolated human SAN cells with a resulting HR of 71.8 bpm. Model validation via simulation of the inhibitory effect of ivabradine showed accordance with experimental results obtained in human studies. Furthermore, we could validate the model in regard to its HR effects upon parasympathetic stimulation with results obtained in a human trial study.

Image-defined Risk Factors Correlate with Surgical Radicality and Local Recurrence in Patients with Neuroblastoma

BACKGROUND

Neuroblastoma is the second most common solid pediatric tumor and the most common cancer to be detected in children younger than 12 months of age. To date, 2 different staging systems describe the extent of the disease: the International Neuroblastoma Staging System (INSS) and the International Neuroblastoma Risk Group Staging System (INRGSS). The INRGSS-system is characterized by the presence or absence of so called image-defined risk factors (IDRFs), which are described as surgical risk factors. We hypothesized that IDRFs correlate with surgical complications, surgical radicality, local recurrence and overall survival (OS).

PATIENTS AND METHODS

Between 2003 and 2010, 102 patients had neuroblastoma surgery performed in our department. We analyzed medical records for IDRF-status and above named data.

RESULTS

16 patients were IDRF-negative, whereas 86 patients showed one or more IDRF. Intra- or postoperative complications have been reported in 21 patients (21%). 19 of them showed one or more IDRF and 2 patients were IDRF-negative (p=n.s.). Patients who suffered from intra- or postoperative complications demonstrated a decreased OS (p=0.011). Statistical analysis revealed an inverse correlation between the extent of macroscopical removal and IDRF-status (p=0.001). Furthermore, the number of IDRFs were associated with a decreased likelihood of radical tumor resection (p<0.001). 19 patients had local recurrence; all of them were IDRF-positive (p=0.037).

CONCLUSIONS

Pediatric surgeons should consider IDRFs as a useful tool for risk assessment and therefore planning for neuroblastoma surgery.

Laparoscopic Adrenalectomy is Feasible for Suspected Adrenal Tumors in Children Younger than 24 Months of Age - But is it Always Justified?

INTRODUCTION

Tumors of the adrenal gland are rare in children younger than 24 months of age. While neuroblastomas are most important in this age group, adrenal hemorrhage and other tumors are sometimes difficult to distinguish. Harvesting biopsies is mandatory in these young patients to obtain information on molecular markers, namely, MYCN and 1p deletion.

PATIENTS

Between 03/2012 and 10/2013, 11 patients younger than 24 months of age with suspicious adrenal tumors were operated on laparoscopically.

METHODS

The diagnostic workup was coordinated by our pediatric oncologists according to the terms of the NB2004 trial protocol.

RESULTS

9 out of 11 had a diagnosis of neuroblastoma, the others were adenoma respective complete necrosis of the adrenal gland. All of the neuroblastomas were negative for both MYCN amplification and 1p deletion. A complete resection was successful in 9 out of 11 cases. 3 complications occurred, 1 major and 2 minor.

DISCUSSION AND CONCLUSION

Behind the recognition that laparoscopic adrenalectomy is technically feasible, the fact that all neuroblastomas were negative for MYCN amplification and 1p deletion raises the issue of whether biopsy is mandatory for risk stratification in this age group.

The associations between postpartum serum haptoglobin concentration and metabolic status, calving difficulties, retained fetal membranes, and metritis

Measurement of serum haptoglobin (Hapto) concentrations results in only moderate reported specificity and sensitivity for the detection of metritic cows. The objective of this study was to evaluate associations between different variables and haptoglobin concentrations after calving. Parity, periparturient metabolic stress indicated by β-hydroxybutyric acid (BHBA) and nonesterified fatty acids (NEFA), calving difficulties, retained fetal membranes (RFM), and acute puerperal metritis (APM) were evaluated. A total of 443 Holstein Friesian cows were enrolled in this retrospective observational study. Acute puerperal metritis was diagnosed when a cow had fetid, reddish-brown, watery vaginal discharge in combination with rectal temperature ≥39.5°C. The retention of the fetal membranes has been defined as the failure to expel the fetal membranes within 12h after calving. Results of blood samples from 2 and 5 d in milk (DIM) were analyzed for Hapto, BHBA, and NEFA. Primiparous cows had a greater median Hapto concentration than multiparous cows at 5 DIM [primiparous: 2.25g/L, interquartile range (IQR) 1.45-2.50, n=146; multiparous: 1.13g/L, IQR 0.52-2.22, n=302; P<0.05]. Therefore, different Hapto thresholds based on references from literature for all cows (1.4g/L), primiparous cows (2.49g/L), and multiparous cows (1.4g/L) were used for further analysis. Periparturient metabolic stress indicated by elevated BHBA (≥1.2mmol/L) at 5 DIM was associated with elevated Hapto (odds ratio 2.39-2.87) regardless of parity. In contrast, elevated NEFA (≥0.6mmol/L) at 2 DIM was not a risk factor for elevated Hapto. Multiparous cows with assisted calving had a 2.46 times higher risk for elevated Hapto, whereas primiparous cows with assisted calving had no elevated risk for elevated Hapto at 5 DIM. Moreover, multiparous cows with RFM were 5.51 times more likely to have elevated Hapto at 5 DIM than cows without RFM. Acute puerperal metritis within the first 5 DIM was associated with elevated Hapto (odds ratio 2.74-5.01), regardless of parity. We speculate that the association of calving ease, RFM, and periparturient metabolic stress could explain the moderate sensitivity and specificity reported for the detection of metritic cows by measuring Hapto.

Technical note: Assessment of milk temperature measured by automatic milking systems as an indicator of body temperature and fever in dairy cows

The objective of this study was to evaluate whether milk temperature (MT) measured by automatic milking system (AMS) is a reliable indicator of body temperature of dairy cows and whether cows with fever could be detected. Data loggers (Minilog 8, Vemco Ltd., Halifax, NS, Canada) measuring body temperature were inserted for 7 ± 1 d into the vaginal cavity of 31 dairy cows and programmed to take 1 reading/min. Milk temperature was recorded at each milking event by the AMS, and values from the vaginal loggers were paired with the corresponding MT. The correlation (r) between vaginal temperature (VT) and MT was 0.52. Vaginal temperature was higher (39.1 ± 0.4°C) than MT (38.6 ± 0.7°C) with a mean difference of 0.5 ± 0.6°C. The ability of MT to identify cows with fever was assessed using 2 approaches. In the first approach, VT could indicate fever at any time of the day, whereas MT could display fever only during the milking events of a given day. Different definitions of fever based on thresholds of VT and duration exceeding these thresholds were constructed. Different thresholds of MT were tested to distinguish between cows with and without fever. The combination of 39.0°C as a threshold for MT and 39.5°C for at least 2h/d as a threshold for VT resulted in the highest combination of sensitivity (0.65) and specificity (0.65). In the second approach, we evaluated whether MT could identify cows with fever at a given milking event. A threshold of MT >38.7°C delivered the best combination of sensitivity (0.77) and specificity (0.66) when fever was defined as VT ≥39.5°C. Therefore, MT measured by AMS can be indicative of fever in dairy cows to a limited extent.

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy

PURPOSE

recent studies have found that KRAS mutations predict resistance to monoclonal antibodies targeting the epidermal growth factor receptor in metastatic colorectal cancer (mCRC). A polymorphism in a let-7 microRNA complementary site (lcs6) in the KRAS 3' untranslated region (UTR) is associated with an increased cancer risk in non-small-cell lung cancer and reduced overall survival (OS) in oral cancers. We tested the hypothesis whether this polymorphism may be associated with clinical outcome in KRAS wild-type (KRASwt) mCRC patients treated with cetuximab monotherapy.

PATIENTS AND METHODS

the presence of KRAS let-7 lcs6 polymorphism was evaluated in 130 mCRC patients who were enrolled in a phase II study of cetuximab monotherapy (IMCL-0144). Genomic DNA was extracted from dissected formalin-fixed paraffin-embedded tumor tissue, KRAS mutation status and polymorphism were assessed using direct sequencing and PCR restriction fragment length polymorphism technique.

RESULTS

KRAS let-7 lcs6 polymorphism was found to be related to object response rate (ORR) in mCRC patients whose tumors had KRASwt. The 12 KRASwt patients harboring at least a variant G allele (TG or GG) had a 42% ORR compared with a 9% ORR in 55 KRASwt patients with let-7 lcs6 TT genotype (P = 0.02, Fisher's exact test). KRASwt patients with TG/GG genotypes had trend of longer median progression-free survival (3.9 versus 1.3 months) and OS (10.7 versus 6.4 months) compared to those with TT genotypes.

CONCLUSIONS

these results are the first to indicate that the KRAS 3'UTR polymorphism may predict for cetuximab responsiveness in KRASwt mCRC patients, which warrants validation in other clinical trials.

A let-7 microRNA-binding site polymorphism in 3'-untranslated region of KRAS gene predicts response in wild-type KRAS patients with metastatic colorectal cancer treated with cetuximab monotherapy

PURPOSE

recent studies have found that KRAS mutations predict resistance to monoclonal antibodies targeting the epidermal growth factor receptor in metastatic colorectal cancer (mCRC). A polymorphism in a let-7 microRNA complementary site (lcs6) in the KRAS 3' untranslated region (UTR) is associated with an increased cancer risk in non-small-cell lung cancer and reduced overall survival (OS) in oral cancers. We tested the hypothesis whether this polymorphism may be associated with clinical outcome in KRAS wild-type (KRASwt) mCRC patients treated with cetuximab monotherapy.

PATIENTS AND METHODS

the presence of KRAS let-7 lcs6 polymorphism was evaluated in 130 mCRC patients who were enrolled in a phase II study of cetuximab monotherapy (IMCL-0144). Genomic DNA was extracted from dissected formalin-fixed paraffin-embedded tumor tissue, KRAS mutation status and polymorphism were assessed using direct sequencing and PCR restriction fragment length polymorphism technique.

RESULTS

KRAS let-7 lcs6 polymorphism was found to be related to object response rate (ORR) in mCRC patients whose tumors had KRASwt. The 12 KRASwt patients harboring at least a variant G allele (TG or GG) had a 42% ORR compared with a 9% ORR in 55 KRASwt patients with let-7 lcs6 TT genotype (P = 0.02, Fisher's exact test). KRASwt patients with TG/GG genotypes had trend of longer median progression-free survival (3.9 versus 1.3 months) and OS (10.7 versus 6.4 months) compared to those with TT genotypes.

CONCLUSIONS

these results are the first to indicate that the KRAS 3'UTR polymorphism may predict for cetuximab responsiveness in KRASwt mCRC patients, which warrants validation in other clinical trials.

Pharmacogenetic profiling of Aurora kinase B is associated with overall survival in metastatic colorectal cancer

Aurora kinases are conserved eukaryotic serine-threonine kinases, which serve as key regulators of mammalian mitosis. Several studies revealed a distinct correlation between inaccurate chromosome segregation, leading to chromosomal number instability, cancer progression and poor outcome. The aim of this study was to investigate the correlation of Aurora kinases A (AURKA) and B (AURKB) with overall survival (OS) by quantifying gene expression analysis and evaluation of single-nucleotide polymorphisms (SNPs) in human colorectal cancer samples and assessing the associations with clinicopathological features. We evaluated intratumoral gene expression levels and SNPs of AURKA and -B from 41 patients with metastatic colorectal cancer (mCRC). Patients with a high expression level of AURKB (>1.28) lived significantly shorter (n=11, median OS=6.4 months, 95% confidence interval (CI): 3.0-14.5 months) compared with patients with a low expression level (≤ 1.28) (n=30, median OS=18.4 months, 95% CI: 14.7-27.8 months, P=0.026, Wald's test). Patients harboring any G-allele in AURKB 885A>G showed a significantly decreased OS (P=0.05, log-rank test). We did not find any associations with clinicopathological variables and AURKA gene expression levels. Our results suggest a potential role for AURKB inhibition in patients with mCRC; thereby supporting its potential role as a target in mCRC.

Genetic variations in angiogenesis pathway genes associated with clinical outcome in localized gastric adenocarcinoma

BACKGROUND

Angiogenesis has been attributed to be a well-recognized aspect of human cancer biology. As such, proteinase-activated receptor (PAR)-1, endostatin (ES) and interleukin-8 (IL-8) mediate the regulation of early-onset angiogenesis and in turn impact the process of tumor-growth and disease progression.

PATIENTS AND METHODS

Formalin-fixed paraffin-embedded tissues were obtained from 137 patients with localized gastric cancer at University of Southern California and Memorial Sloan-Kettering Cancer Center medical facilities. DNA was extracted and genotyping was carried out using PCR-restriction fragment length polymorphism-based protocols.

RESULTS

In false discovery rate-adjusted univariate analysis, PAR-1 -506 ins/del (P < 0.001), ES +4349 G>A (P = 0.004), and IL-8 -251 T>A (P < 0.0001) were associated with time to tumor recurrence (TTR). Further, PAR-1 -506 ins/del and IL-8 -251 were associated with overall survival (OS). After adjusting for covariates, IL-8 remained significantly associated with TTR (adjusted P = 0.003) and OS (adjusted P = 0.049), whereas ES was significantly associated with TTR (adjusted P = 0.026).

CONCLUSIONS

Polymorphisms in PAR-1, ES, and IL-8 may serve as independent molecular prognostic markers in patients with localized gastric adenocarcinoma. The assessment of the patients' individual risk on the basis of interindividual genotypes may therefore help to identify patient subgroups at high risk for poor clinical outcome.

Association of gender, age, and ethnicity with survival in patients with pancreas cancer

e15587

Background: Pancreatic cancer (PC) is the fourth leading cause of cancer death in the United States. However little is still known about factors that influence its development and progression. Recent data suggest that PC is, at least in part, an estrogen- dependent disease; there is growing epidemiological evidence that aspects of reproductive history and hormonal exposure are associated with risk of this disease. It was shown that age at menarche of <13 is associated with less risk of PC. However no data are available whether gender is associated with outcome in patients with PC. The purpose of this study was to test whether age, gender or ethnicity influence the outcome in PC. Methods: The data of the 50,302 adults diagnosed with PC between 1988 and 2004 were extracted from the Surveillance Epidemiology and End Results public use database. These included 24,240 patients diagnosed with localized pancreatic cancer (LPC) and 26,062 patients with metastatic pancreatic cancer (MPC). Demographic, clinical variables and survival time were retrieved. The primary endpoint was overall survival. We constructed Cox proportional hazards models to evaluate association between patient characteristics and survival in LPC and MPC separately. Pair interactions were also tested. Results: On multivariate analysis gender, age, race, marital status, tumor size, grade, histology, type of treatment and lymph node involvement were found to be independent predictors of survival. Females had a significant longer survival, with an HR of 0.959 (95% CI: 0.932–0.987) among patients with LPC and an HR of 0.918 (95%CI: 0.894–0.942) among patients with MPC. Each age group displayed a significant longer survival than its correspondent older age group. When we combined age and gender in the analysis, females had a longer survival than males in each single age group in the MPC group. In the LPC group the longer survival of female patients was only observed in the youngest age group. Conclusions: This is the first and largest study to address gender and outcome in PC. Our data suggest that the estrogen pathway may play an important prognostic role in patient with this disease. These data also warrant further in vitro and in vivo investigations on the mechanisms of estrogen and pancreas progression.

No significant financial relationships to disclose.

Colorectal cancer susceptibility variants and clinical outcome in adjuvant and metastatic colorectal cancer

4051

Background: Recent genome-wide association studies had identified colorectal cancer susceptibility loci on chromosomes 8q24 (rs6983267), 15q13(rs4779584), 18q21(rs4939827, rs12953717 and rs4464148), 10p14(rs10795668) and 8q23.3(rs16892766). Although the function role of these germline variants are unclear, given the importance of these variants and colorectal cancer risk, we have carried out the first pilot study to explore the association of these variants and clinical outcome. We used pooled data from two CRC-cohorts (locally advanced and metastatic CRC), and investigated the hypothesis that these germline variants may be associated with clinical outcome in adjuvant and metastatic colorectal cancer patients. Methods: Whole blood was collected from 515 patients with locally advanced (n=197) and metastatic CRC (n=318). After extraction of genomic-DNA, germline variants were genotyped as previously described (Haiman et al, Nat Genet, 2007). The genotype success rate was 98%. Blinded repeat samples (5%) were included for quality control purposes; genotype concordance was ≥ 99%. Results: Our results suggest that rs10795668 at 10p14 and rs719725 are significantly associated with time to tumor recurrence in adjuvant colorectal cancer patients, patients with rs10795668 AA genotype had significantly increased risk of time to tumor recurrence compared with those harboring G allele (TG+GG) patients(p=0.05, log-rank test). In metastatic cancer patients, we found rs4939827 at 18q21.1 were significantly associated with overall survival in female patients and rs10795668 at 10p14 were significantly associated with OS in male patients, respectively (p<0.05). Conclusions: Our preliminary results suggest cancer risk alleles may also associated with clinical outcome in adjuvant and metastatic colorectal cancer. Moreover, this correlation is sex-specific in metastatic colorectal cancer. Further comprehensive trials warranted to confirm our pilot findings.

[Table: see text]

Wt Kras and gene expression levels of VEGFR2, EGFR, and ERCC-1 associated with progression-free survival (PFS) in patients (pts) with metastatic colorectal cancer (mCRC) treated with first-line 5-FU or capecitabine with oxaliplatin and bevacizumab (FOLFOX/BV or XELOX/BV)

4056

Background: While wild type (wt) Kras is associated with improved outcome to anti-EGFR therapy in pts with mCRC, there are no identified predictors of outcome for FOLFOX/BV. We evaluated Kras status and expression of genes involved in angiogenesis, DNA repair and 5-FU metabolism in 68 patients treated with FOLFOX/BV or XELOX/BV. These genes included VEGF, VEGF-receptor 2 (KDR), Cox-2, IL 6 and 8, chemokine-receptors 1 & 2, EGFR and ERCC-1. Methods: Tissue samples from 68 patients with mCRC were analyzed. mRNA was extracted from laser-capture-microdissected tumor tissue. cDNA was prepared by reverse transcription and quantitation of the candidate genes was performed using a fluorescence- based real-time detection method (TaqMan). Allele specific RT-PCR was performed to determine Kras mutation status in codons 12 and 13. Results: There were 68 pts (38 males, 30 females), median age: 56 years (range 29–81). All received first line 5FU, oxaliplatin and BV (28 FOLFOX/BV, 40 XELOX/BV). Radiologic response: 1 CR, 39/68 (57%) PR, 27/68 (40%) SD, and 1 PD. Median OS is not reached. At a median follow-up of 32.0 months (mo) (range: 2.3–47.8 mo), the median PFS was 12.4 mo (95% CI: 9.8–15.2). Kras mutation was identified in 39 pts (57%). RR was 64% in pts with wt Kras and 52% in pts with mutant Kras (p=0.33). PFS was significantly longer for pts with wt kras compared to pts with mutant kras (13.7 mo [95% CI: 6.9–13.2] versus 8.3 mo [95%CI: 6.9–13.2], P=0.039). High EGFR (median PFS: 15.2 mo; 95% CI 11.7–16.5 mo), high VEGFR2 (median PFS: 13.9 mo; 95% CI 11.0–16.5 mo), and low ERCC1 (median PFS: 12.4 mo; 95% CI 10.9–16.4 mo) were associated with longer PFS compared to low EGFR (median PFS: 7.9 mo; 95% CI 6.9–11.0 mo, P=0.040), low VEGFR2 (median PFS: 7.2 mo; 95% CI 6.5–8.1 mo, P=0.032), and high ERCC1 (median PFS: 9.6 mo; 95% CI 5.8–15.2 mo, P=0.045). Conclusions: To our knowledge, this is the first report of a potential association between Kras status as well as gene expression levels of VEGFR2, ERCC-1 and EGFR and clinical outcome to FOLFOX/BV therapy in pts with mCRC. Prospective clinical trials are needed to validate these results.

[Table: see text]

Pharmacogenetic analysis in metastatic colorectal cancer (mCRC) patients (pts) treated with second-line irinotecan (IR)+/− cetuximab (CB): The EPIC experience

4022

Background: EPIC, a multinational phase III clinical trial with IR + CB vs IR alone in mCRC pts in the second-line setting after failure of FOLFOX demonstrated a benefit for IR+CB in progression-free survival (PFS) and response rate (RR). We evaluated functional germline polymorphisms involved in the EGFR- (EGF, EGFR), angiogenesis- (VEGF, IL-8, CXCR-2) - and drug- metabolism related genes (UGT1A1, MTHFR) for their potential role as molecular predictors for clinical outcome in pts treated with CB/IR vs. IR alone. Methods: DNA was extracted from all available formalin-fixed paraffin-embedded tumor samples from the phase III EPIC trial (US sites only). Genotyping was performed using PCR-RFLP assays and 5’ -end [g-33P] ATP’ labeled PCR-protocols. Results: 186 pts were treated either with IR/CB (arm A, 84 pts) or IR (arm B, 102 pts) only. In arm A, 11/84 pts (13%) showed CR or PR, whereas 73/84 (87%) pts had SD or PD. For arm B, 6/102 pts (6%) showed CR or PR, whereas 96/102 pts (94%) had SD or PD. Median PFS in arm A was 3.0 months (95%CI: 2.4- 4.1 months) vs 2.7 months (95%CI: 2.2–2.9 months) in arm B; median overall survival (OS) was 9.3 months (95%CI: 7.1–12.1 months) in arm A vs. 12.3 months (95%CI: 10.4- 17.9 months) in arm B. K-ras mutation status was not significantly associated with PFS or response to CB/IR in the subgroup of 186 patients. We found an EGFR-CA- repeat in intron 1 in arm A to be associated with PFS (p=0.031, log-rank test). In arm B, we found a significant association with RR (p=0.0103, Fisher's exact test) for MTHFR1298. Furthermore, MTHFR 677 (p =0.0048, log-rank test) and MTHFR 1298 (p=0.038, log-rank test) were also found to be associated with OS in arm B. In multivariate analysis, EGFR-CA-repeat was significantly associated with PFS (adjusted p= 0.023). Furthermore, MTHFR 677 and MTHFR 1298 was associated with OS (adjusted p=0.028 and 0.026, respectively, Cox-proportional hazards models), independent from K-ras mutation status, race and number of disease sites. Conclusions: Our study demonstrates the potential predictive value of polymorphisms in the EGFR- and MTHFR- gene in mCRC pts treated with IR+ CB. Further validation in additional clinical trials is necessary.

[Table: see text]

Effect of gender and age on overall survival in patients with esophageal cancer

4541

Background: The American Cancer Society estimated that during 2008 approximately 16,470 new esophageal cancer cases would be diagnosed in the United States. Previous studies indicate that the incidence of esophageal cancer is more in males than females; however the influence of sex in the progression of esophageal cancer is not clearly understood. In vitro and in vivo models showed that administration of estradiol significantly inhibited the growth of ER-positive and AR-positive KSE-1 tumors in both males and females in conjunction with an increase in the estradiol levels and a decrease in the DHT levels in the serum. Thus we tested the clinical significance of sex in the overall survival of esophageal cancer using SEER data. Methods: A total of 21,584 patients with localized and metastatic esophageal cancer from 1988–2004 were screened using the SEER registry. The patients were divided into age at diagnosis, sex and ethnicity. The analysis for overall survival was based on the Cox proportional hazards model adjusted for marital status, site of primary tumor, treatment, histology and tumor grade and stratified by year of diagnosis and SEER registry site. Pairwise interactions (age and sex, age and race, and sex and race) were also examined. Results: Females with localized esophageal cancer had significantly longer overall survival compared to males (p<0.001). In metastatic esophageal cancer, females seemed to have longer overall survival than males (p=0.054). Overall survival decreased with increasing age (p<0.001). African Americans with localized esophageal cancer have worse median overall survival compared to Caucasians (p<0.001). No significant difference was noted with respect to ethnicity in metastatic esophageal cancer (p=0.22). Also pairwise interactions did not have significant difference. Conclusions: This is the first and largest study showing gender as an independent prognostic factor in patients with localized and metastatic esophageal cancer. Females had a significant better overall survival than males in esophageal cancer suggesting that sex hormone pathways may have a potential impact on tumor progression. These data warrant further studies to explore the role of these pathways in the diagnosis and treatment of esophageal cancer.

No significant financial relationships to disclose.

Association of CD133 polymorphisms and clinical outcome in metastatic colorectal cancer (mCRC) patients (pts) treated with either first-line 5-FU + bevacizumab (BV) or second-line irinotecan (IR)/cetuximab (CB) or IR alone

4062

Background: CD133 has been routinely used to identify colon cancer stem cells. A recent study indicated that elevated levels of CD133 plasma mRNA correlated with colon cancer recurrence. Furthermore plasma levels of CD133+ progenitor cells have been found to be decreased after treatment with BV. We tested whether potentially functional frequently occurring germline variations in the 3’UTR-region of the CD133 gene (rs2240688, rs3130 and rs2286455), might be associated with clinical outcome in first- and second-line treated mCRC pts. Methods: Genomic DNA was extracted either from peripheral blood (79 pts, who were enrolled in a phase-II clinical trial with FOLFOX/BV or XELOX/BV) or formalin-fixed paraffin-embedded tumor samples (186 pts, who were enrolled in the EPIC phase III clinical trial, US-sites only) of mCRC pts. Pts received either first-line treatment with FOLFOX/ BV (33 pts) or XELOX/BV (46 pts) or second-line treatment with CB/IR (84 pts, arm A) or IR (102 pts, arm B) alone. Genotyping was performed using PCR-RFLP assays. Results: 79 pts (47 men, 32 women) received FOLFOX/BV or XELOX/BV. Radiologic response: 43 pts (54%) CR/PR, 35 pts (45%) SD/PD. Median PFS was 10.8 months (95%CI: 8.1–14.9). The second cohort consisted of 186 pts (103 men, 83 women). Radiologic response: Arm A 11 pts (13%) CR/PR, 73 pts (87%) SD/PD. Arm B 6 pts (6%) CR/PR, 96 pts (94%) SD/PD. Median PFS (arm A) was 3.0 months (95%CI: 2.4–4.1) vs. 2.7 months (arm B,95%CI: 2.2–2.9). Combined analysis of rs2286455 and rs3130 showed a significant association with PFS (p= 0.010, log-rank test) in pts receiving FOLFOX/BV or XELOX/BV. In pts receiving IR alone rs2240688 was significantly associated with OS (p=0.0128, log-rank test). Multivariate analysis showed a significant association with PFS in first-line setting for rs2286455 and rs3130 (adjusted p=0.012) and a trend in second-line setting for rs2240688 (adjusted p=0.086). Conclusions: These are the first data to show that polymorphisms in CD133 predict outcome in mCRC pts in first- and second- line setting, suggesting that CD133 may be a potential predictive marker. These results need to be confirmed in larger prospective studies.

[Table: see text]

Association of a germ-line variant in the K-ras 3’ untranslated region with response and progression-free survival in patients with mCRC treated with single-agent cetuximab (IMCL-0144) or in combination with cetuximab (EPIC) independent of K-ras mutation status

4061

Background: Recent studies have found K-ras mutation status predicts response to EGFR inhibitors in mCRC. An in vitro study demonstrated let-7 microRNA family can regulate RAS expression by binding to the 3’UTR of RAS gene. Chin et al found a SNP in a let-7 microRNA complementary site (LCS) in the K-ras 3’ UTR increases cancer risk in NSCLC. We tested the hypothesis whether this SNP may be associated with clinical outcome in 130 mCRC patients enrolled in IMCL-0144 trial and in 186 pts enrolled in EPIC trial independent of K-Ras mutation status in the tumor. Methods: K-ras lcs 6 SNP was tested in 130 mCRC patients enrolled in IMC-0144 phase II clinical trial (single agent cetuximab) and in 186 mCRC patients enrolled in a second line phase III trial of cetuximab plus irinotecan versus irinotecan alone (EPIC). Genomic DNA was extracted from dissected formalin fixed paraffin embedded tumor tissue and K-ras mutation status and the polymorphism were analyzed using direct sequencing and PCR-RFLP technique. Results: The G harboring allele frequency in K-ras lcs6 was 8% in IMC-0144 and 11% in EPIC. K-ras lcs6 polymorphism was significantly associated with tumor response in patients with wild type K-ras in IMC-0144. The 12 pts harboring a G allele (TG+GG) had a 42% partial response (PR) rate compared to 55 pts with TT genotype with only 9% PR.(p=0.02, Fisher's-exact test). However, pts with TT genotype enrolled in EPIC treated with CPT-11 and cetuximab with mutant K-ras had a significantly better PFS of 12 weeks (95% CI 6.4–18) compared to those harboring the a G allele with median PFS of 6.4 weeks (95% 5.7–7) (p=0.037. log-rank test). There was no association between this polymorphism and clinical outcome in patients with wild type K-ras enrolled in EPIC. In a multivariate analysis the polymorphism remained independently associated with PFS in EPIC. Conclusions: Our data suggest for the first time that the functional germline polymorphism in K-ras lcs6 may be a potential predictive marker in mCRC patients treated with cetuximab-based chemotherapy independent of K-ras mutation status. This finding warranted further confirmative clinical trials.

[Table: see text]

Polymorphisms in epidermal growth factor (EGF) and proteinase activated receptor 1 (PAR-1) associated with tumor recurrence in localized adenocarcinoma (EA) of the esophagus treated with surgery alone

4564

Background: Tumor angiogenesis is a well-recognized aspect of human cancer biology and is mediated at least in part by EGF and PAR-1, which in turn may impact the process of tumor growth and progression. Systemic tumor recurrence after curative resection continues to be a significant problem in the management of patients with localized EA. Further, it is being increasingly recognized that esophageal squamous cell carcinoma and EA are separate and distinct disease groups and need to be considered individually. We therefore designed a large retrospective study of EA patients to identify novel molecular markers of prognosis to better define tumor stage and progression, and help to define novel targets, as well as surrogate-endpoints of disease progression and response to therapy. Methods: Between 1992 and 2005 normal esophageal tissue samples from 239 patients with localized EA treated with surgery alone were obtained at University of Southern California medical facilities. The median follow-up was 3.2 years. 114 out of 239 (48%) patients had tumor recurrence, with a probability of 5-year recurrence of 0.62 ± 0.04. DNA was isolated from formalin-fixed paraffin-embedded specimens and 10 angiogenesis related and functional gene polymorphisms were analyzed using a PCR-RFLP and 5´-end [γ-33P] ATP-labeled PCR method. Results: PAR-1 -506 ins/del (p-value=0.003; log-rank test) and EGF +61 A>G (p-value=0.034; log-rank test) are adverse prognostic markers in univariate analysis. After adjusting for covariates (gender, T1-, N-category, type of surgery) in the multivariable model, "high-expression" variants of PAR-1 (any insertion allele) (RR: 1.81; adjusted p-value = 0.011) and EGF (A/A) (RR: 1; adjusted p-value=0.035) remained significantly associated with time to recurrence, compared to other genotype combinations of PAR-1 (RR: 1) and EGF (RR: 0.65). Conclusions: This study supports the role of functional EGF and PAR-1 polymorphisms as independent prognostic markers in localized EA and may therefore help to identify patient subgroups at high risk for tumor recurrence. Prospective and biomarker-embedded clinical trials are needed to validate our findings.

[Table: see text]

VEGF and VEGFR1 gene expression levels and tumor recurrence in adjuvant colon cancer

4040

Background: Tumor recurrence after curative resection is still a major problem in the management of adjuvant colon cancer, with recurrence rate approximately 30–40%. Identifying molecular markers for tumor recurrence is critical for successfully selecting patients who are more likely to benefit from adjuvant chemotherapy. Our group previously showed that angiogenesis gene polymorphisms (VEGF and IL-8) may associated with tumor recurrence in adjuvant colon cancer (Lurje Ann Oncol, 2008). Here we tested the hypothesis whether gene expression levels of angiogenesis pathway (COX-2, EGFR, VEGF, VEGFR1, VEGFR2 and IL-8) could also predict the risk of tumor recurrence in stage II and III colon cancer patients treated with adjuvant chemotherapy. Methods: Tissue samples from 140 adjuvant colon cancer patients (69 females and 71 males with a median age of 59 years; range=28–86) were available for gene expression assays. These tissue samples were obtained at the University of Southern California/Norris Comprehensive Cancer Center (USC/NCCC) and LAC+USC medical center between 1999 and 2006. Sixty-three patients had stage II and 77 had stage III colon cancer. The median follow-up was 5.4 years (range=2.0–16.8). 51 of 140 patients (36.4%) developed tumor recurrence with a 5-year probability of 0.28 ± 0.06 for stage II and 0.40 ± 0.06 for stage III colon cancer patients. mRNA was extracted from laser-capture-microdissected tumor tissue. After cDNA was prepared by reverse transcription, quantitation of the candidate genes and an internal reference gene (ß-actin) was performed using a fluorescence-based real-time detection method (TaqMan). Results: We found VEGF and VEGFR1 gene expression levels independently significantly associated with time to tumor recurrence in adjuvant colon cancer patients. Patients with lower VEGF gene expression and lower VEGFR1 gene expression levels had significantly longer time to tumor recurrence compared to those with higher VEGF and higher VEGFR1 gene expression levels (p<0.05, log-rank test). Conclusions: VEGF and VEGFR1 gene expression levels may predict tumor recurrence risk in adjuvant colon cancer patients. Our exploratory data warrant future confirmatory trial.

[Table: see text]

Use of genetic variants to predict clinical outcome in patients (pts) with metastatic colorectal cancer (mCRC) treated with first-line 5-FU or capecitabine in combination with oxaliplatin and bevacizumab (FOLFOX/BV or XELOX/BV)

4070

Background: Recent studies suggested polymorphisms involved in angiogenesis related genes associated with clinical outcome in pts treated with the VEGF-inhibitor bevacizumab. (Schneider et al. JCO 2008, Manegold et al ASCO 2008). We evaluated functional polymorphisms involved in angiogenesis- (VEGF, KDR, IL-6, CXCR1 and-2), apoptosis (p53) and cell-proliferation (MMP2,-7 and-9, ICAM)-related pathways in an expanded patient cohort for their potential prognostic or predictive role in clinical outcome. Methods: Genomic DNA was extracted from 79 mCRC pts (treated with first-line FOLFOX/BV or XELOX/BV at USC) from peripheral blood. Genotyping was performed using PCR-RFLP assays or direct sequencing. Results: 79 pts (47 men, 32 women) with a median age of 56 years (range 29–81), were treated with either FOLFOX/BV (33 pts) or XELOX/BV (46 pts). Radiologic response: 2/79 pts (3%) CR, 41/79 pts (52%) PR, 32/79 pts (41%) SD and 3/79 pts (4%) DP. At a median follow-up of 32.0 months (range: 1.4- 47.8 months), the median time to progression was 10.8 months (95% CI: 8.1–14.9). We found IL-6 G- 174C (p=0.025, Fisher's exact test) and p53 codon 72 (p=0.029, Fisher's exact test) polymorphisms associated with response to BV-therapy. Furthermore, there were statistically significant associations between genomic polymorphisms in MMP-9, CXCR-1 and PFS (p=0.023 and p=0.014, respectively, log-rank test). Pts with 2 G- alleles in CXCR-1 G+2607C (median PFS=13.7 months, 95% CI:8.4–16.4) and pts homozygous for the C-allele in MMP-9 C-1562T (median PFS= 13.9 months, 95% CI: 10.1–15.8) had longer PFS compared to pts with any C-allele in CXCR-1 G+2607C (median PFS = 7.9 months, 95% CI: 6.9–10.2) and pts with any T-allele in MMP-9 C-1562T (median PFS 7.2 months, 95% CI: 5.3–11.0), respectively. Conclusions: These are the first data to predict clinical outcome in mCRC pts treated with FOLFOX/BV or XELOX/BV. Our data demonstrate that functional polymorphisms in angiogenesis related genes predict response and PFS in pts treated with the angiogenesis- inhibitor BV. However, confirmation of these findings in larger, prospective genotype-guided clinical trials is warranted.

[Table: see text]

The UCSC Genome Browser Database: update 2009

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

The UCSC Genome Browser Database: 2008 update

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

Modes of administration of antibiotics for symptomatic severe urinary tract infections

BACKGROUND

Urinary tract infection (UTI), worldwide, is a major source of disease in children and adults. As it may have long-term consequences such as kidney failure and hypertension, it is important to treat patients with UTI adequately. Although standard management of severe UTI usually means intravenous (IV) therapy, at least initially, there are studies showing that oral therapy may also be effective.

OBJECTIVES

To assess whether the mode of administration of antibiotic therapy for severe UTI has an effect on cure rate, reinfection rate and kidney scarring.

SEARCH STRATEGY

The Cochrane Renal Group's specialised register, the Cochrane Central Register of Controlled Trials (CENTRAL, in The Cochrane Library), MEDLINE and EMBASE were searched. No language restriction was applied. Reference lists of relevant articles and reviews were checked for additional studies and authors of relevant articles/abstracts were contacted for further information. Date of last search: July 2007.

SELECTION CRITERIA

All randomised controlled trials (RCTs) comparing different modes of antibiotic application for patients with severe UTI (children and adults) were considered.

DATA COLLECTION AND ANALYSIS

Study quality was assessed and data extracted. Statistical analyses were performed using the random effects model and the results expressed as relative risk (RR) for dichotomous outcomes or mean difference (WMD) for continuous data with 95% confidence intervals (CI).

MAIN RESULTS

Fifteen RCTs (1743 patients) were included. Studies compared oral versus parenteral treatment (1), oral versus switch treatment (initial intravenous (IV) or intramuscular (IM) therapy followed by oral therapy) (5), switch versus parenteral treatment (6) and single dose parenteral followed by oral therapy versus oral (1) or switch therapy (3). There was a variety of short-term and long-term outcomes, but no pooled outcomes showed significant differences. Most included studies were small though and there were few outcomes for combination in a meta-analysis.

AUTHORS' CONCLUSIONS

There is no evidence suggesting that oral antibiotic therapy is less effective for treatment of severe UTI than parenteral or initial parenteral therapy. The results of this review suggest that the mode of application does not determine therapeutic success.

The UCSC genome browser database: update 2007

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at .